In the organisms, every response is regulated at both cis- and trans-directions. The bidirectional regulation sustains the balances and the orders of vital movements of organisms. This kind of regulation is certain to concern two related modulating molecules. According to the frugal theory of organic evolution, after a molecule accomplishes the regulation of one direction, allosterism or the change of its primary structure will change and it will turn to attenuate or inhibit the reaction once promoted by it and it also becomes the modulating molecule of the other direction. These chromatin peptides and their antecedent transcription factors are mutually rivalry on functions and the molecules from same origin accomplish the bidirectional regulation at cis- and trans-directions with this mode.
Tens of thousands of people are pinched to death by malignant tumors every year, besides, some people have a closed bout with death and survive with tumor for many years and even are healed. Otherwise, more people with cancer cells in their bodies appear no symptom. It is believed that there are tens (approximately 30-100) mutated pre-cancer cells are generated in human body everyday. But those mutated pre-cancer cells are eliminated in human body everyday and endlessly. So that, those people do not get sick despite the unceasing generation of cancer cells under most conditions. The human body itself displays the inhibiting and even healing capacity of anti-cancer. After all, what kind of mode does the body use to cure many cancer patients? What is the mechanism of the cancer escaping from the control of the body and causing the death of the patients? We found that there are some chromatin peptides with bioactivity in human body and they are the DNA-binding domain fragments of some transcription factors which specifically recognize and bind with the characteristic regulatory elements/gene promoters in the process of gene transcription and activate the gene transcription; then allosterism happens and the molecules break away from the regulatory elements; when the domino-like cascade of downstream genes driven by transcription factors is constrained by some external conditions, for example, once the oxygen supply is blocked (hypoxia), the expressed transcription factors will accumulate excessively, leading to proteasome response and these factors will be degraded into chromatin peptides. Those chromatin peptides maintain the specific affinity of them with its DNA substrate, which have the capacity of binding with the regulated downstream genes and block the expression of these genes as a negative feedback. The excessive transcriptions of many proto-oncogenes which initiate tumorigenesis/aggravation all block the overexpression of their own or their downstream regulating genes through the intrinsic “broken-key blocking effect” of the organisms so that the cellular malignant proliferation are firmly blocked; maybe this is the fundamental reason causing the healing or long-term with tumor survival of many cancer patients; more patients die of cellular excessive expression caused by the continuous overexpression of those malignant genes, which may be caused by the deficient of chromatin peptides inducing “the broken-key blocking effect” to close the over-expression of those malignant genes in their bodies. Therefore, it is hopeful to make it the best way to cure cancer if we can block the over-expression of malignant genes by synthesizing and supplying these chromatin peptides or their bionic molecules and then block the cellular malignant proliferation of the tumor. Here we found some chromatin peptides possessing the functions described above.
Compared with another natural drugs generated by organism itself such as antibodies, chromatin peptides have many similarities with them, and also, they have their special functions, respectively, and serve for the health maintenance of the body and the continue of life from different aspects: antibody is a kind of protein which recognizes and binds with specific antigens of some exogenous pathogens and causes complement response, degrades and eliminates the pathogen which is harmful for the body; the body can encode more than 60 thousand kinds of antibodies aiming at different antigens through gene recombination and only a trifle of them are generously cloned and utilized: once the body is invaded by certain pathogen, the antibody will specifically recognize and bind with the antigen just as a stamp to a key, and then the cell secreting the conformal antibody which combines with the antigen in the form of lock-key mosaic structure will be cloned and utilized; thus, immune response and antibody are the professional physiological functions defending the invasion of exogenous pathogens generated during the evolution of life. Chromatin peptides are a group of oligopeptides generated by the degradation of transcription factor, recognizing and binding with the specific DNA structural domain sequences of this transcription factor itself and those downstream genes driven by it and blocking these promoters in order to block the uncontrollable expression of these genes; the cellular automatic growth and proliferation are essentially a kind of domino-like reactions related with the gene expression regulated by its chromatin template, and once the reaction network is interfered and blocked by some exogenetic and/or endogenetic factors (e.g., hypoxia without adequate supply of ATP to initiate the cellular disjunction action chain), the upstream of the gene expression cascade will accumulate excessive transcription factor and then activates the proteasome lytic response, which can degrade these junk, in which, the fragment of the transcription factor recognizing and binding with its DNA substrate, the DNA-binding domain, is reserved and binds with the DNA substrate, blocks and closes the uncontrollable gene expression cascade and the cellular growth/proliferation just like the “handle-breaking key” blocks the lock hole and prevents the other keys from opening the door. We call it “the broken-key blocking effect”. Therefore, “the broken-key blocking effect” of gene transcription factor and its chromatin peptides belongs to a kind of biological function to defend the uncontrollable gene expression caused by endogenetic gene mutation generated during evolution of life. On the whole, both antibodies and chromatin peptides have the biological functions of guarding body and maintaining life: antibodies, responsible for outside, are in charge of counteracting the exogenetic invasions and decreasing the exogenetic pathogens below the tolerable level of the body; chromatin peptides, responsible for inside, are in charge of suppressing the endogenetic rebellions and inhibiting the over-expression of the malignant genes below the tolerable level of the body. Both of the two kinds of defending mechanisms are according to the mode of “gaining mastery by striking only after the enemy has struck”. The immune response will not be activated and selectively clone adequate corresponding antibodies until excessive proliferation of pathogens has reached certain quantity, meanwhile, the “the broken-key blocking effect” is initiated and produces adequate chromatin peptides through the degradation only when the malignant transcription factor is excessively accumulated. However, these autochthonous defending capacities of life sometimes can not beat all enemies and maintain permanent living; supplying and enhancing the autochthonous defending capacities of life may maintain the longer livening of life through vaccination and supplement of chromatin peptides. As we all know, people controlled many lethal diseased caused by exogenetic pathogens—bacteria and viruses through vaccine injection 100 years ago. Now, we can control the endogenetic pathogen-malignant cellular diseases by supplying the related chromatin peptides.
In the last few years, considerable studies have accumulated many evidences from multiple aspects which suggest that the orgasms have obtained the above-mentioned “the broken-key blocking effect” of proteins and the chromatin peptides defending mechanism during the evolution, and the chromatin peptides, blocking the malignant cells and the malignant progressive proliferation as well as the cellular hypoxia biological response, really exist in organisms.
The relationship between the transcription factor and its derivative chromatin peptides is functional rivalry. The functional rivalry phenomenon of protein/derivative peptides includes: the promoters of HIF-1α/C-FOS/C-Myc, three promoter genes of cell proliferation, all have the histogeneous cis-transcription modulation elements (Trans-transcription modulation elements for histodifferentiation), the erythrogenic Cis-NFE2 element in HIF-1α, the B cell cytogenous Cis-MITF element in C-FOS and the T cell cytogenous Cis-NFAT element in C-Myc. It is clear that in the process of cellular development and maturation, when they initiate the functional gene group of histodifferentiation, they also block the binding site of embryonic stem cell transcription factors on the chromatin structure of HIF-1α/C-FOS/C-Myc gene transcription activity so that the chromatin phenotype is recombined and the progressive proliferation phenotype of embryonic stem cell is recombined to the kinetic equilibrium proliferation phenotype of maturity differentiated cell.
The proliferation of many malignant tumor cells may stop when they proliferate to certain quantity. Through the view of the mechanism, initiation of cell proliferation needs adequate oxygen and nutrients, however, to drive the continuous over-expression of those upstream malignant genes does not need generous energy. Therefore, hypoxia can only directly cause the arrest of the downstream proliferation genes but can not directly induce the cease of the continuous excessive transcription of the upstream malignant genes; for this reason, deficiency of energy directly leads to the arrest of the downstream proliferation genes and the terminating signal sent out by the downstream genes indirectly induces the transcription cease of the upstream malignant genes; this terminating signal is transferred and accomplished by chromatin peptides produced by proteasome response initiated by the excessive accumulation of malignant transcription factor.
The specific recognition and binding of protein/protein or protein/DNA are the basic modes of biological molecular communication activities. The combination of them is usually the combination of mosaicism among rigid structures/key-lock mode and the sequences of these domains are usually composed of hydrophobic amino acids. The hydrophobic region makes them difficult to be degraded by proteases at their dissociation state. This part of domains is also hard to approach for proteases and difficult to be degraded once they bind with each other. These structures are able to escape from the proteasome response due to these chemical characteristics of these domains, and the hydrophobic peptides also have longer half life than their complete sequence proteins which make the effective efficiency dose much lower. Otherwise, the chromatin peptides which we choose for drug treatment contain more basic amino acids, which is profit for them to get concentrated in the subacidity circumstance of tumor tissue.
The binding of regulatory subunit/domain between these two kinds of complete sequence molecules may initiate the allosterism of functional subunit and exertion of the function and then these two kinds of molecules separate with each other to achieve the dynamic functions or cis-regulation/trans-regulation functions of information transfer. Some static and long-term cis-regulation/trans-regulation phenotype combination will form as soon as the domain of a kind of degrading molecules binding with the domain of another kind of complete sequence molecules. Accordingly, the binding equilibration of chromatin peptides/transcription factor forms a type of physiological stabilized status. On the other hand, “the broken-key blocking effect” of gene expression network is a type of stabilizing effect of cellular chromatin template and growth phenotype which arrests cells at stable phenotype. Status from dynamic fluctuation to static stabilization is the dynamic equilibrium theory of cell proliferation. In summary, the cellular automatic proliferation is restrained in a limited space inside of the cells; the movements of orientation composed of two domino-like reactions between gene expression and expressed product proteins are actually a kind of switch reactions including many gene groups: a gene group is initiated and then it will be silent after action followed by the initiation of the downstream gene groups; each protein needs to degrade itself once accomplished the positive function and spares space for the later actions; sometimes it is necessary to close the expression or the function of this protein in order to enter the reaction of the next protein. So, during the long-term evolution, the organisms have constructed a kind of protein molecular mechanism which accomplish the initiation of one function and close two switch actions with “labor-saving” coordinating effect.
The traditional killing therapy aims directly at the cells in vegetative state. Virtually, many important healthy cells, including marrow, epithelial cells, etc, are all proliferating faster than some tumor cells. These therapies are all on the cost of sacrificing more healthy cells; this is the common shortage of traditional chemotherapy, radiotherapy and traditional Chinese medicine therapy. Immunotherapy and gene therapy have selectivity to act with malignant cells, particularly, the anti-vascularization reaction therapy even does not injury normal cells. The reason why the immunotherapy does not have the intended effect may be contributed to the absence of specific immunogen in tumor cells under a majority of conditions. The forthcoming studies suggest that, there is only quantitative difference but no qualitative difference between the antigens of autogenetic malignant tumors and that of normal cells. The above-mentioned gene therapy without intended effect may have chosen wrong drug target: the drug target is localized on the gene products, the dynamic mRNA or protein which immediately disappeared after the quick expression, which may only change and interfere the cellular malignant state temporarily but can not change and block its malignant phenotype permanently. The only way to change and block the cellular malignant phenotype to achieve the radical cure is to localize the drug target on the DNA level through stabilized static standard domino-like reactions and the regulatory elements of gene expression.
Now some people have realized the importance of blocking malignant genes. At present, the hot point of researches is to block malignant genes through RNAi. People have gained some effects under experimental conditions. However, there still exist some difficulties hard to overcome, including stability, permeating transportation of cellular membrane and nuclear membrane, etc so that there are great difficulties in the practical application. Some other ways blocking gene by chemicals are also difficult to apply to medical practice because of bad specificity.
Transcription factor of HIF-1α is mentioned in three comments in Nature, volume May, 2003, which described the hypoxia inducing factor initiating a group of genes, exerting some emergency treatment functions (Kirsty Minton THERAPEUTICS: It's suffocating in here! Nature Reviews May 2003 Vol 3 No 5): once the ischemic happened because of injury in some part of the body, firstly, it will initiate the glycolytic pathway in that tissue, like an ambulance of the body, and it will generate ATP as the energy resource under the condition without oxygen and provide the energy to the almost suffocated cells to offer relief assistance; meanwhile, it will shift the immunologic cells, including macrophages, heterophil granulocytes, etc., by biological emergency signals to eliminate dead cells and intercellular substances in order to provide living environment for those survival cells. It will also simulate the growth of the blood capillaries in the surrounding tissue to grow toward this area by biological repairing signals to transfer blood to the anoxic tissue. It is properly that that ambulance process which becomes a criminal when the tumor cells begin malignant growth and the chronic inflammation cells begin proliferating: it initiates the glycolytic pathway in tumor cells and produce ATP to assist the almost suffocated cancers cells because of hypoxia; it also calls for immune inflammatory reaction to eliminate necrosis tissue in order to provide the growth space and the chance of invasion for those survival cancer cells. Otherwise, it even leads to the growth of cancer cells to this area to supply those cancer cells with new oxygen provision and the metastasis chance. On the whole, our bodies have not generated the intelligence to clearly distinguish right and wrong during evolution: the ambulance, initiated by HIF-1α transcription factor, not only assists the injury of normal tissue but also assist those tumor cells to escape from the suffocating state caused by the above-mentioned chromatin peptides “broken-key blocking effect” without hesitation and leads to the pathogenetic condition aggravation and death of some cancer patients.
Under what kind of conditions does the malignant proliferation of tumor cells initiate the blocking effect of chromatin peptides and achieve the self-healing of the body, and under what kind of conditions does it fail to initiate the blocking effect and escape from the control of the body? Oxygen is the first restriction factor of cell proliferation: during cell proliferation, the cell density increases in the limited space with the increase of cell population and the provision of oxygen and glucose decreases by and by so that the cell proliferation slows down till stops. In short, the relationship between the capacity of cell proliferation and the cell population is inverse proportion and the final proliferation and blocking may give out a determined cell population and the size of tumor tissue. The typical physiological case is skin: basal cells, the most inner layer of skin, are close to vessels, obtain adequate oxygen and proliferate toward the exterior by and by, and the speed of proliferation slows down with the decrease of oxygen till the end cell of epidermis, which stop splitting because of oxygen deficiency and enter the necrosis state with karyopyknosis.
The typical pathological case is hypoxia of tumor: mutations of some signal genes lead the cells to escape the control of outside signals, for example, the loss of contact inhibition, and the cells will continuously proliferate, and they will stop proliferating or enter the apoptotic state or enter resting state when the oxygen decreases to a critical point. The molecular mechanism of the cell proliferation blocking caused by the above-mentioned minimum critical point of oxygen is probably as following: the transcription factors of MYC group initiate their downstream cell proliferation gene group and promote the domino-like reactions of the downstream cell proliferation genes and set them onto the cell division pathway, and the reaction will cease once the oxygen reduce to a critical point; the transcription factors of MYC group will induce/activate proteasome response once they are accumulated to a maximal critical point, which will degrade these cell proliferation initiating molecules and those cellular apoptosis related shutting off molecules into chromatin peptides in order to block the expression of these cell proliferation promoting transcription factors. If “the broken-key blocking effect” of MYC group drops out “the broken-key blocking effect” of HIF-1α group will restrict the nutrient and energy provision of tumor cells. The outcome of long-term human evolution makes the body have multistrata and multipath capacity to resist the uncontrollable proliferation of malignant cells and this is the mechanism of system autogenetic-healing. The chromosome mutation or gene mutation in some tissue cells will induce the dropout of HIF-1α hypoxia inducing pathway and the cellular malignant proliferation, invasion and metastasis will escape from the blocking caused by asphyxiant chromatin peptides through the following HIF-1α dropout steps: first of all, HIF-1α switches on the glycolytic pathway of tumor cells, which increases the resistance of cells to hypoxia circumstances and makes the tumor move into the in situ progressive proliferation step; subsequently, it induces the immune inflammatory reaction to eliminate the necrotic tissue and provides the living space and the chance of invasion for those survival cancer cells, which makes the tumor move into the in situ invasion stage; finally, it even induces the growth of blood vessels toward the cancer tissue to provide new oxygen provision and the chance of invasion for those cancer cells, which makes the tumor move into the heterotopic metastasis and rapid aggravation stage. The initiation and blocking of these cellular malignant proliferations are both accomplished through cell proliferation promoting transcription factor and the chromatin peptides produced by its degradation in “the broken-key blocking effect”. The chromatin peptides produced through transcription factors of MYC group and those chromatin peptides produced through transcription factors of HIF-1α group block the cellular malignant genesis and metastasis and alleviate the cellular malignant proliferation, invasion and metastasis.
It is especially necessary to point out that there exists large difference on the nutrient and energy provision and requirement between malignant tumor cells and normal cells. Some data suggest that the cell needs much more energy and nutrients to grow than to maintain its activity. However, the malignant cancer cell needs much more nutrient and energy than normally growing cells because of its much faster uncontrollable growth rate. Judah Folkman, a famous surgeon, found that the genesis of malignant tumor is followed by angiogenesis of large quantity of blood vessels and it is one of the ways for tumor cells to enlarge their oxygen provision in order to increase the energy and nutrient provision. On the other hand, the malignant cell initiates anaerobic metabolism—glycolytic pathway and increases the permeation speed of oxygen and glucose through the cellular membrane and blood vessel to retrieve the deficiency of oxygen and energy. Folkman proposed the conception of anti-angiogenesis therapy, which relies on confining the oxygen and energy provision of malignant tumor cells. However, some drug target of present anti-angiogenesis therapy is angiogenin, a gene product for stimulating angiogenesis; some proteins inhibiting tumor angiogenesis, for example, Endostatin, Angiostatin, etc., mainly produce a marked effect through the rivalry with angiogenesis stimulating factors, for example, VEGF. Those therapies do not cut off the origins of angiogenin or VEGF—the encoding genes of that, making it necessary to continuously complement anti-angiogenesis materials.
The patient's pathogenetic condition will get worse till death once the proliferation and metastasis of tumor cells lose control. For this point of view, no matter how aggravated has the patient's pathogenetic condition been, it may be stabilized and the patient's life may be saved so long as you block the cellular malignancy pathway by the chromatin peptides obtained from the degradation of transcription factors such as HIF-1α On the other hand, there are some other mechanisms of the initiation of cellular malignant proliferation besides HIF-1α pathway. However, the malignant growth of any entity tumor must break through the restriction of energy and nutrient. Therefore, the expression of HIF-1α transcription factor and its regulating transcription factors are necessary for the malignant growth of any entity tumor. With regard to the tumor malignant growth caused by the breakthrough of the oxygen restriction leaded by HIF-1α and anchoring-dependent and contact inhibition pathways regulated by MYC group, the blocking agents we designed can not only realize the cellular phenotype transformation from malignant phenotype to normal cellular phenotype but also lead to the death or apoptosis of tumor tissue because of absence of oxygen and energy. According to those malignant tumors caused by the other mechanisms, it mainly induces the death or apoptosis of cancer cells by the restriction of nutrient, oxygen and energy.
To sum up, we described the function of HIF-1α, a hypoxia restriction factor, in human body and its function during the genesis of malignant tumor; and analyzed the functional antagonism between chromatin peptides, produced by the degradation of the related transcription factor, and their derivative precurosors and “the broken-key blocking effect” produced by the binding between chromatin peptides and the silencer/enhancer/promoter of the gene chromosome plate. On these foundations, we have tested chromatin peptides as the drug treating symptoms and getting at the root to cure malignant tumors and carried out a serial of trials to verity their pharmacodynamic actions and safety.